Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-4775
Title: Progressive multiple sequence alignment with indel evolution
Authors : Maiolo, Massimo
Zhang, Xiaolei
Gil, Manuel
Anisimova, Maria
Published in : BMC bioinformatics
Volume(Issue) : 19
Issue : 331
Publisher / Ed. Institution : BioMed Central
Issue Date: 2018
License (according to publishing contract) : CC BY 4.0: Attribution 4.0 International
Type of review: Peer review (Publication)
Language : English
Subjects : Dynamic programming; Indel; Phylogeny; Poisson process; Probability; Sequence alignment; Algorithms; Molecular evolution; INDEL mutation
Subject (DDC) : 572: Biochemistry
Abstract: Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modelled by a Markov substitution model. In contrast, the dynamics of indels are not modelled explicitly, because the computation of the marginal likelihood under such models has exponential time complexity in the number of taxa. But the failure to model indel evolution may lead to artificially short alignments due to biased indel placement, inconsistent with phylogenetic relationship.
Departement: Life Sciences and Facility Management
Organisational Unit: Institute of Applied Simulation (IAS)
Publication type: Article in scientific Journal
DOI : 10.21256/zhaw-4775
10.1186/s12859-018-2357-1
ISSN: 1471-2105
URI: https://digitalcollection.zhaw.ch/handle/11475/14486
Appears in Collections:Publikationen Life Sciences und Facility Management

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